BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080901.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 5,072,937 number of mapped reads = 4,606,032 (90.8%) number of supplementary alignments = 41,350 (0.82%) number of secondary alignments = 0 number of mapped bases = 314,800,115 bp number of sequenced bases = 314,685,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 247,592 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9331 >>>>>>> ACTG content number of A's = 90,063,996 bp (28.62%) number of C's = 55,349,860 bp (17.59%) number of T's = 101,285,353 bp (32.19%) number of G's = 66,456,500 bp (21.12%) number of N's = 1,529,896 bp (0.49%) GC percentage = 38.71% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 3,598,368 number of insertions = 24,091 mapped reads with insertion percentage = 0.52% number of deletions = 69,908 mapped reads with deletion percentage = 1.5% homopolymer indels = 50.2% >>>>>>> Coverage mean coverageData = 0.1017X std coverageData = 0.6333X There is a 7.07% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 23413881 0.09393710196613712 0.8501343736266901 chr2 243199373 28790620 0.11838278875825885 0.6385210650245584 chr3 198022430 22167802 0.11194591440979691 0.45128304141055153 chr4 191154276 22035691 0.11527699751796293 0.4746001739107786 chr5 180915260 20295319 0.11218135496143332 0.45489161327846045 chr6 171115067 19113085 0.11169726509238372 0.5674014885451185 chr7 159138663 18045098 0.1133922936125208 0.8761768766805305 chr8 146364022 17004221 0.11617760135069259 1.2605627866174236 chr9 141213431 13192163 0.0934200302802642 0.5977211510323708 chr10 135534747 14153142 0.1044244543430623 0.5460380413633533 chr11 135006516 13798403 0.10220545947574856 0.5847374351677888 chr12 133851895 14710681 0.10990267265173945 0.4557879184207121 chr13 115169878 10422510 0.09049683980736699 0.40864915954436404 chr14 107349540 9446561 0.0879981507140133 0.4329749916812784 chr15 102531392 8195542 0.07993202706152668 0.38235707168472155 chr16 90354753 7470770 0.0826826453722916 0.41833105657034936 chr17 81195210 7300424 0.08991200342975897 0.45612056491310815 chr18 78077248 8482057 0.10863673115117992 1.0743507830170609 chr19 59128983 4549516 0.0769422332191981 0.5969084882881661 chr20 63025520 5829325 0.09249150185512155 0.4307680140164293 chr21 48129895 4015413 0.08342866735944468 0.4293461837280842 chr22 51304566 2643362 0.0515229385236394 0.30240211638966347 chrMT 16571 45914 2.7707440709673525 2.7908283855512073 chrX 155270560 19026998 0.1225409246930004 0.5080968870576857 chrY 59373566 651617 0.010974867165633945 0.17941117215226443